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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGATCCTTGGCATCATTTCCACTCAGCGGCTTCCTTTCCCCTCCAACTCATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTGgtaattcctctcttccatataatgataagtctcagatgtaaatttggacaaaattacattatcaataagttgtcgctgaggttcattggttgatcatata...

Basic information

species Vitis vinifera
transcript Vv02s0033g01120.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0033g01120.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA09G34640.1 (Glycine max), 5'ss of exon 4
GCGATCCTTGGCATCATTTCCACTCAGCGGCTTCCTTTCCCCTCCAACTCATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTGgtaattcctctcttc-catataatgataagtctcagatgtaaatttggacaaaattacattatcaataagttgtcgctgaggttcattggttgatcatata---
||  | |||||  ||||||| || ||| | ||||||||||| || ||||| |||||||||||||||||||| |||||||||||||||||||| |||||||||||||| ||  | |  ||   ||  ||    | | |  |||||    |  || |    ||     ||  ||||   |||  |||  |  |   |  ||     
GCTGTTCTTGGTGTCATTTCTACACAGAGACTTCCTTTCCCATCAAACTCCTTTGATATGGCTCATTGCTCCAGATGCCTTATCCCATGGACAGAATTTGgtaattcttcagtgcatattggattttatcaattaaacataaatc---attaattcttgtttatgctacattgtta-tgaatttctgtaatgagttttaattgg

upper sequence: Vv02s0033g01120.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA01G35220.5 (Glycine max), 5'ss of exon 5
GCGATCCTTGGCATCATTTCCACTCAGCGGCTTCCTTTCCCCTCCAACTCATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTGgtaattcctctcttc-catataatgataagtctcagatgtaaatt----tggacaaaattacattatcaataagttgtcgctgaggttcattggttgatcatata
||  | |||||  ||||||| || ||| | ||||||||||| || ||||| |||||||||||||||||||| |||||||||||||||||||| ||||| |||||||| ||  | |  ||   ||  ||    | | |   ||||     | |   |   || ||| | | | |  | |  |||      | || || |  |    
GCTGTTCTTGGTGTCATTTCTACACAGAGACTTCCTTTCCCATCAAACTCCTTTGATATGGCTCATTGCTCCAGATGCCTTATCCCATGGACAGAATTCGgtaattcttcagtgcatattggattttattggttaaacagaaatcattcttgtttatgctatattgtta-tgaactttgcctgcatgaaactgcttcacaa----

upper sequence: Vv02s0033g01120.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA16G08120.1 (Glycine max), 5'ss of exon 5
GCGATCCTTGGCATCATTTCCACTCAGCGGCTTCCTTTCCCCTCCAACTCATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTGgtaattcctctcttccatataatgataagtctcagatgtaaatttggacaaaattacattatcaataag-ttgtcgctgaggttcattgg-ttgatcatata--
|| || |||||  || |||| || | | | ||||| ||||| || ||||| |||||||||||||||||||| |||||||| ||||||||||| ||||||||||   | | | | |   ||  |||  | | | ||   | ||     | ||  |     | |   | ||  | |  ||   | ||||    || |  | ||   
GCAATTCTTGGTGTCCTTTCTACACGGAGACTTCCATTCCCATCAAACTCCTTTGATATGGCTCATTGCTCCAGATGCCTAATCCCATGGACAGAATTTGgta--ccttttttgctggattttga--acttttagtatttaagaaatagaatttattcctgtttgtgagactctttctagtgatcatgaactttagtacattac

upper sequence: Vv02s0033g01120.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA16G17500.1 (Glycine max), 5'ss of exon 5
GCGATCCTTGGCATCATTTCCACTCAGCGGCTTCCTTTCCCCTCCAACTCATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTGgtaattcctctcttccatat--aatgataagtctcagatgtaaatttggacaaaatta--cattatcaataagttgtcgctgaggttcattggttgatcatata
|| || || ||  ||||||| || ||| | ||||| ||||| || | ||| |||||||||||||||||||| |||||||||||||||||||| |||| ||||| ||  |    |  || |  ||   | ||| ||  |    |||||   |    |||  ||  |    | |||  ||  |||  || | |  || | ||    
GCAATTCTCGGTGTCATTTCTACACAGAGACTTCCATTCCCATCAAGCTCCTTTGATATGGCTCATTGCTCCAGATGCCTTATCCCATGGACAGAATATGgtacttttttctatggattttgaacttttagtatctaaacataatttattcctgtttatgcaacacttttcagtgatca-tgaactttagtactttaccag---

upper sequence: Vv02s0033g01120.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT1G31850.3 (Arabidopsis thaliana), 5'ss of exon 4
GCGATCCTTGGCATCATTTCCACTCAGCGGCTTCCTTTCCCCTCCAACTCATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTGgtaattcctctcttccatataatgataagtctcagatgtaa--atttggacaaaattacattatcaataagttgtcgctgaggtt-cattggttgatcatata
||||| || || ||||| || || || || || ||||| || || ||  ||||||||||||||||||| |||||||| ||||| || ||||| |||||||||||   ||    || |  ||   ||   | | || |||    ||||| || ||     || ||||| | ||  || | ||  || ||               
GCGATTCTCGGGATCATCTCTACGCAACGTCTCCCTTTTCCTTCAAATGCATTTGATATGGCTCATTGTTCAAGATGTCTTATTCCCTGGACAGAATTTGgtaagcactaatatctacctaccaatgcatttgagttgttgtgatttgaactaagaataatcatcaaaatgtgttctccgatcttgcag--------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|110729666|gb|EE105862.1|EE105862
EST:     ATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTG                         GTGGAATATACCTCCTAGAAGTACACCGCATACTCCGCCCTGGAGGGTTCT
genomic: ATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTGgtaattcctc ... ctgttttcagGTGGAATATACCTCCTAGAAGTACACCGCATACTCCGCCCTGGAGGGTTCT
EST: gi|30126183|gb|CB911522.1|CB911522
EST:     ATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTG                         GTGGAATATACCTCCTAGAAGTACACCGCATACTCCGCCCTGGAGGGTTCT
genomic: ATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTGgtaattcctc ... ctgttttcagGTGGAATATACCTCCTAGAAGTACACCGCATACTCCGCCCTGGAGGGTTCT
EST: gi|110719144|gb|EE096785.1|EE096785
EST:     ATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTG                         GTGGAATATACCTCCTAGAAGTACACCGCATACTCCGCCCTGGAGGGTTCT
genomic: ATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTGgtaattcctc ... ctgttttcagGTGGAATATACCTCCTAGAAGTACACCGCATACTCCGCCCTGGAGGGTTCT
EST: gi|110712840|gb|EE088240.1|EE088240
EST:     ATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTG                         GTGGAATATACCTCCTAGAAGTACACCGCATACTCCGCCCTGGAGGGTTCT
genomic: ATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTGgtaattcctc ... ctgttttcagGTGGAATATACCTCCTAGAAGTACACCGCATACTCCGCCCTGGAGGGTTCT
EST: gi|110712136|gb|EE089409.1|EE089409
EST:     ATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTG                         GTGGAATATACCTCCTAGAAGTACACCGCATACTCCGCCCTGGAGGGTTCT
genomic: ATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTGgtaattcctc ... ctgttttcagGTGGAATATACCTCCTAGAAGTACACCGCATACTCCGCCCTGGAGGGTTCT
EST: gi|219555224|gb|FG984925.1|FG984925
EST:     ATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTG                         GTGGAATATACCTCCTAGAAGTA
genomic: ATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTGgtaattcctc ... ctgttttcagGTGGAATATACCTCCTAGAAGTA
EST: gi|110719072|gb|EE096633.1|EE096633
EST:     ATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTG                         GTGGAATATACCTCCTAGAAGTACACCGCATACTCCGCCCTGGAGGGTTCT
genomic: ATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTGgtaattcctc ... ctgttttcagGTGGAATATACCTCCTAGAAGTACACCGCATACTCCGCCCTGGAGGGTTCT
EST: gi|219555419|gb|FG985032.1|FG985032
EST:     ATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTG                         GTGGAATATACCTCCTAGAAGT
genomic: ATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTGgtaattcctc ... ctgttttcagGTGGAATATACCTCCTAGAAGT
EST: gi|219555469|gb|FG984556.1|FG984556
EST:     ATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTG                         GTGGAATATACCTCCTAGAAGTAC
genomic: ATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTGgtaattcctc ... ctgttttcagGTGGAATATACCTCCTAGAAGTAC
EST: gi|219555415|gb|FG985028.1|FG985028
EST:     ATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTG                         GTGGAATATACCTCCTAGAAGTAC
genomic: ATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTGgtaattcctc ... ctgttttcagGTGGAATATACCTCCTAGAAGTAC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGATCCTTGGCATCATTTCCACTCAGCGGCTTCCTTTCCCCTCCAACTCATTTGATATGGCTCATTGCTCAAGATGCCTTATCCCATGGACTGAATTTGgtaattcctctcttccatataatgataagtctcagatgtaaatttggacaaaattacattatcaataagttgtcgctgaggttcattggttgatcatata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gacaaaa